• Proceedings of the Korean Information Science Society Conference
• /
• 2008.06c
• /
• pp.230-235
• /
• 2008

생명정보 대량 획득기술의 하나인 마이크로어레이(microarray)는 DNA와 각종 유적자 연구에 사용되는 도구로서 확립되면서, 생명정보학(bioinformatics)분야의 발전에 크게 기여하였다. 그러나 마이크로어레이는 생명정보학분야의 핵심기술 중 하나로 발전하였음에도 불구하고 마이크로어레이 실험으로 생성되는 데이터는 형태가 다양하고 매우 복잡한 형태를 갖기 때문에 데이터의 공유나 저장에서 많은 어려움을 겪는 것이 사실이다. 따라서 마이크로어레이 실험결과 분석을 위한 최소한의 컨텐츠가 정의되고 표준화 되었다. MIAME 데이터, MAGE-OM/ML과 같은 표준화된 공개 저장소는 전문 생물학 연구단체에게 과거부터 지금까지 주요 관심사가 되어왔다. 하지만 많은 공개저장소의 설립되었지만 마이크로어레이 데이터의 구조적 특징을 고려하여 효과적인 설계를 하지 않은 것이 사실이다. 본 논문은 표준을 따르는 동시에 마이크로어레이 데이터의 구조적 빈발 패턴이 반복되는 계층적 특징을 반영하는 전략을 제안한다. 이를 통하여 복잡한 데이터의 구조를 객체들의 빈발 패턴을 파악하여 그 계층을 줄임으로서 복잡도를 줄일 수 있었다. 이 과정에서 관계형 데이터베이스 기반의 공개저장소의 성능에 영향을 주는 관계 테이블(join-table)의 숫자는 줄어든다. 이에 따라, 성능은 개선된다. 이 전략을 통하여 생성된 테이블의 숫자는 원본 데이터를 단순 매핑시켜 저장하는 방법에 비하여 약 31%줄어든다. 결국 MAGE-ML 데이터의 저장과 로딩 시간은 이 논문에서 제시하는 전략을 적용하지 않은 방법에 비해 60%에서 65%를 줄일 수 있었다.

• BMB Reports
• /
• v.50 no.5
• /
• pp.247-256
• /
• 2017

CRISPR/Cas9 is the latest tool introduced in the field of genome engineering and is so far the best genome-editing tool as compared to its precedents such as, meganucleases, zinc finger nucleases (ZFNs) and transcription activator-like effectors (TALENs). The simple design and assembly of the CRISPR/Cas9 system makes genome editing easy to perform as it uses small guide RNAs that correspond to their DNA targets for high efficiency editing. This has helped open the doors for multiplexible genome targeting in many species that were intractable using old genetic perturbation techniques. Currently, The CRISPR system is revolutionizing the way biological researches are conducted and paves a bright future not only in research but also in medicine and biotechnology. In this review, we evaluated the history, types and structure, the mechanism of action of CRISPR/Cas System. In particular, we focused on the application of this powerful tool in autophagy research.

• Clinical and Experimental Reproductive Medicine
• /
• v.26 no.3
• /
• pp.377-381
• /
• 1999

Objectives: Recent studies, including our own, demonstrated that the novel expression of LH gene in rat gonads and uterus, indicating that the local production and action of the LH-like molecule. In the present study, we investigated whether human uterus also expresses the LH gene. Design: Reverse transcription-polymerase chain reaction (RT-PCR) amplified the cDNA fragments coding $LH_{\beta}$ polypeptide from human endometrium but not from myometrium. Presence of the transcripts for the ${\alpha}$-subunit in human endometrium was also confirmed by RT-PCR. Results: Transcripts for $LH_{\beta}$ subunit were detected in endometrial samples from women with endometriosis. The gene for LH/hCG receptor was expressed in both endometrium and myometrium, showing good agreement with previous studies. Increased level of $LH_{\beta}$ transcript was determined in the endometrium from follicular phase compared to that from luteal phase. Conclusion: Taken together, our findings demonstrated that 1) the genes for LH subunits and LH/hCG receptor are expressed in human uterus, 2) the uterine LH expression was changed during menstrual cycle, suggesting that the uterine LH may playa local role in the control of uterine physiology and function(s).

• Journal of Microbiology and Biotechnology
• /
• v.29 no.5
• /
• pp.667-686
• /
• 2019

Streptomyces are attractive microbial cell factories that have industrial capability to produce a wide array of bioactive secondary metabolites. However, the genetic potential of the Streptomyces species has not been fully utilized because most of their secondary metabolite biosynthetic gene clusters (SM-BGCs) are silent under laboratory culture conditions. In an effort to activate SM-BGCs encoded in Streptomyces genomes, synthetic biology has emerged as a robust strategy to understand, design, and engineer the biosynthetic capability of Streptomyces secondary metabolites. In this regard, diverse synthetic biology tools have been developed for Streptomyces species with technical advances in DNA synthesis, sequencing, and editing. Here, we review recent progress in the development of synthetic biology tools for the production of novel secondary metabolites in Streptomyces, including genomic elements and genome engineering tools for Streptomyces, the heterologous gene expression strategy of designed biosynthetic gene clusters in the Streptomyces chassis strain, and future directions to expand diversity of novel secondary metabolites.

• The Journal of Korea Institute of Information, Electronics, and Communication Technology
• /
• v.14 no.6
• /
• pp.487-496
• /
• 2021

The analysis method of the microbiome has been evolving for a very long time, and the industrial field has grown rapidly with the start of human genome analysis 20 years ago. As continuous research continues, related industries have grown together, and among them, Illumina of the US has been leading the popularization of DNA analysis by developing innovative equipment and analysis methods since its establishment in 1998. In this paper, 'AiB Index', 'AiB Chart' using statistical process control and log-scale technique to analyze the gut microbiome analysis methodology and implement an algorithm that can analyze minute changes in the minor strains that can be overlooked in the existing analysis methods. want to implement. From the data analysis point of view, we proposed a platform for analyzing gut microbes that can collect fecal data, match and process gut microbes, and store and visualize the results.

• Journal of Microbiology and Biotechnology
• /
• v.28 no.1
• /
• pp.1-11
• /
• 2018

An antioxidant peptide derived from Pinctada fucata meat using an Alcalase2.4L enzymatic hydrolysis method (named AOP) and identified by LC-TOF-MS has promising clinical potential for generating cosmetic products that protect skin from sunshine. To date, there have been few published studies investigating the structure-activity relationship in these peptides. To prepare antioxidant peptides better and improve their stability, the design and expression of an antioxidant peptide from Pinctada fucata (named DSAOP) was studied. The peptide contains a common precursor of an expression vector containing an ${\alpha}$-helix tandemly linked according to the BamHI restriction sites. The DNA fragments encoding DSAOP were synthesized and subcloned into the expression vector pET-30a (+), and the peptide was expressed mostly as soluble protein in recombinant Escherichia coli. Meanwhile, the DPPH radical scavenging activity, superoxide radical scavenging activity, and hydroxyl radical scavenging activity of DSAOP $IC_{50}$ values were $0.136{\pm}0.006$, $0.625{\pm}0.025$, and $0.306{\pm}0.015mg/ml$, respectively, with 2-fold higher DPPH radical scavenging activity compared with chemosynthesized AOP (p < 0.05), as well as higher superoxide radical scavenging activity compared with natural AOP (p < 0.05). This preparation method was at the international advanced level. Furthermore, pilot-scale production results showed that DSAOP was expressed successfully in fermenter cultures, which indicated that the design strategy and expression methods would be useful for obtaining substantial amounts of stable peptides at low costs. These results showed that DSAOP produced with recombinant Escherichia coli could be useful in cosmetic skin care products, health foods, and pharmaceuticals.

• Biotechnology and Bioprocess Engineering:BBE
• /
• v.11 no.4
• /
• pp.319-324
• /
• 2006

Although the sera used in animal cell culture media provide the macromolecules, nutrients, hormones, and growth factors necessary to support cell growth, it could also be an obstacle to the production of recombinant proteins in animal cell culture systems used in many sectors of the biotechnology industry. For this reason, many research groups, including our laboratory, have been trying to develop serum-free media (SFM) or serum-supplemented media (SSM) for special or multi-purpose cell lines. The Chinese hamster ovary (CHO) cell, for example, is frequently used to produce proteins and is especially valuable in the large-scale production of pharmaceutically important proteins, yet information about its genome is lacking. Also, SFMs have only been evaluated by comparing growth patterns for cells grown in SFMs with those grown in SSM or by measuring the titer of the target protein obtained from cells grown in each type of medium. These are not reliable methods of obtaining the type of information needed to determine whether an SFM should be replaced with an SSM. We carried out a cDNA microarray analysis to evaluate MED-3, an SFM developed in our laboratory, as a CHO culture medium When CHO cells were cultured in MED-3 instead of an SSM, several genes associated with cell growth were down-regulated, although this change diminished over time. We found that the insulin-like growth factor (IGF) gene was representative of the proteins that were down-regulated in cells cultured in MED-3. When several key supplements - including insulin, transferrin, ethanolamine, and selenium - were removed from MED-3, the IGF expression was consistently down- regulated and cell growth decreased proportionately. Based on these results, we concluded that when an SFM is used as a culture medium, it is important to supplement it with substances that can help the cells maintain a high level of IGF expression. The data presented in this study, therefore, might provide useful information for the design and development of SFM or SSM, as well as for the design of genome-based studies of CHO cells to determine how they can be used optimally for protein production in pharmaceutical and biomedical research.

• Proceedings of the Korean Society of Crop Science Conference
• /
• 2017.06a
• /
• pp.14-14
• /
• 2017

The discipline of plant breeding is experiencing a renaissance impacting crop improvement as a result of new technologies, however fundamental questions remain for predicting the phenotype and how the environment and genetics shape it. Inexpensive DNA sequencing, genotyping, new statistical methods, high throughput phenotyping and gene-editing are revolutionizing breeding methods and strategies for improving both quantitative and qualitative traits. Genomic selection (GS) models use genome-wide markers to predict performance for both phenotyped and non-phenotyped individuals. Aerial and ground imaging systems generate data on correlated traits such as canopy temperature and normalized difference vegetative index that can be combined with genotypes in multivariate models to further increase prediction accuracy and reduce the cost of advanced trials with limited replication in time and space. Design of a GS training population is crucial to the accuracy of prediction models and can be affected by many factors including population structure and composition. Prediction models can incorporate performance over multiple environments and assess GxE effects to identify a highly predictive subset of environments. We have developed a methodology for analyzing unbalanced datasets using genome-wide marker effects to group environments and identify outlier environments. Environmental covariates can be identified using a crop model and used in a GS model to predict GxE in unobserved environments and to predict performance in climate change scenarios. These new tools and knowledge challenge the plant breeder to ask the right questions and choose the tools that are appropriate for their crop and target traits. Contemporary plant breeding requires teams of people with expertise in genetics, phenotyping and statistics to improve efficiency and increase prediction accuracy in terms of genotypes, experimental design and environment sampling.

• Genomics & Informatics
• /
• v.21 no.3
• /
• pp.42.1-42.23
• /
• 2023

Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis, one of the most deadly infections in humans. The emergence of multidrug-resistant and extensively drug-resistant Mtb strains presents a global challenge. Mtb has shown resistance to many frontline antibiotics, including rifampicin, kanamycin, isoniazid, and capreomycin. The only licensed vaccine, Bacille Calmette-Guerin, does not efficiently protect against adult pulmonary tuberculosis. Therefore, it is urgently necessary to develop new vaccines to prevent infections caused by these strains. We used a subtractive proteomics approach on 23 virulent Mtb strains and identified a conserved membrane protein (MmpL4, NP_214964.1) as both a potential drug target and vaccine candidate. MmpL4 is a non-homologous essential protein in the host and is involved in the pathogen-specific pathway. Furthermore, MmpL4 shows no homology with anti-targets and has limited homology to human gut microflora, potentially reducing the likelihood of adverse effects and cross-reactivity if therapeutics specific to this protein are developed. Subsequently, we constructed a highly soluble, safe, antigenic, and stable multi-subunit vaccine from the MmpL4 protein using immunoinformatics. Molecular dynamics simulations revealed the stability of the vaccine-bound Tolllike receptor-4 complex on a nanosecond scale, and immune simulations indicated strong primary and secondary immune responses in the host. Therefore, our study identifies a new target that could expedite the design of effective therapeutics, and the designed vaccine should be validated. Future directions include an extensive molecular interaction analysis, in silico cloning, wet-lab experiments, and evaluation and comparison of the designed candidate as both a DNA vaccine and protein vaccine.

• Pediatric Gastroenterology, Hepatology & Nutrition
• /
• v.4 no.2
• /
• pp.155-160
• /
• 2001

Purpose: Helicobacter pylori has been known to have diverse vacA allelic types. The purpose of the study was to identify vacA diversity in Korea and design new primers for signal sequence alleles indigenous to Korea. Methods: Fifty antral biopsy specimens, which had been proven to be H. pylori-positive, were examined for vacA status; signal sequence and mid-region. After PCR amplification and DNA sequencing, vacA alleles of Korean H. pylori strains were compared with those from other countries. Results: Among Korean H. pylori strains vacA alleles with all combinations of signal sequence and mid-region were found, with the exception of s1b or s2. vacA genotype s1c/m1 was predominant in Korea. We found that GGGAGCGTTR in s1a and GGGGYTATTG in s1c were the indigenous sequences to Korea and constructed the new Korean specific primers for the vacA signal sequence; VASK-F, VASK-R, S1AK-F, and S1CK-F. Conclusion: This study showed that s1c/m1 is the predominant type of vacA allele in Korea. We designed new primers for the vacA signal sequence.